| import ast |
| import csv |
| import json |
| import os |
| import random |
| from collections import defaultdict |
| from multiprocessing import Pool |
|
|
| from PIL import Image |
|
|
| BASE_DIR = "./VindrMammo" |
| CSV_PATH = os.path.join(BASE_DIR, "vindr_detection_v1_folds.csv") |
| IMG_DIR = os.path.join(BASE_DIR, "images_png") |
| CROP_DIR = os.path.join(BASE_DIR, "crop") |
|
|
| OUTPUT_TRAIN_JSON = os.path.join(BASE_DIR, "VinDr-Mammo_train.json") |
| OUTPUT_TEST_JSON = os.path.join(BASE_DIR, "VinDr-Mammo_test.json") |
|
|
| MIN_SIZE = 28 |
| IOU_THR = 0.5 |
| CONTAIN_THR = 0.7 |
| NUM_WORKERS = 8 |
| MAX_TEST_SAMPLES = 1000 |
| RANDOM_SEED = 42 |
|
|
|
|
| def area(b): |
| return max(0, b[2] - b[0]) * max(0, b[3] - b[1]) |
|
|
| def intersect_area(a, b): |
| ix1 = max(a[0], b[0]); iy1 = max(a[1], b[1]) |
| ix2 = min(a[2], b[2]); iy2 = min(a[3], b[3]) |
| return max(0, ix2 - ix1) * max(0, iy2 - iy1) |
|
|
| def should_merge(a, b): |
| inter = intersect_area(a, b) |
| if inter == 0: |
| return False |
| iou = inter / (area(a) + area(b) - inter) |
| contain = inter / min(area(a), area(b)) |
| return iou >= IOU_THR or contain >= CONTAIN_THR |
|
|
| def union_box(boxes): |
| return (min(b[0] for b in boxes), min(b[1] for b in boxes), |
| max(b[2] for b in boxes), max(b[3] for b in boxes)) |
|
|
| def merge_boxes(boxes): |
| boxes = list(boxes) |
| changed = True |
| while changed: |
| changed = False |
| for i in range(len(boxes)): |
| for j in range(i + 1, len(boxes)): |
| if should_merge(boxes[i], boxes[j]): |
| merged = union_box([boxes[i], boxes[j]]) |
| boxes = [boxes[k] for k in range(len(boxes)) if k not in (i, j)] |
| boxes.append(merged) |
| changed = True |
| break |
| if changed: |
| break |
| return boxes |
|
|
|
|
| def crop_with_min_size(img, x_min, y_min, x_max, y_max, min_size=MIN_SIZE): |
| cx = (x_min + x_max) // 2 |
| cy = (y_min + y_max) // 2 |
| w = max(x_max - x_min, min_size) |
| h = max(y_max - y_min, min_size) |
| x_min = max(0, cx - w // 2); x_max = min(img.width, x_min + w); x_min = max(0, x_max - w) |
| y_min = max(0, cy - h // 2); y_max = min(img.height, y_min + h); y_min = max(0, y_max - h) |
| return img.crop((x_min, y_min, x_max, y_max)) |
|
|
|
|
| def normalize_path(path): |
| return str(path).replace("\\", "/") |
|
|
| def remove_root_prefix(path, root): |
| path = normalize_path(path) |
| root = normalize_path(root).rstrip("/") |
| if path.startswith(root + "/"): |
| return path[len(root) + 1:] |
| elif path == root: |
| return "" |
| return path |
|
|
|
|
| def process_group(args): |
| key, before_boxes, class_id, patient_id, split = args |
| image_id, class_name = key |
| img_path = os.path.join(IMG_DIR, patient_id, image_id + ".png") |
|
|
| try: |
| img = Image.open(img_path) |
| except Exception as e: |
| return None, f"open {image_id}: {e}" |
|
|
| after_boxes = merge_boxes(before_boxes) |
|
|
| crop_paths = [] |
| for idx, box in enumerate(after_boxes): |
| crop_name = f"{image_id}_{class_id}_{idx}.png" |
| crop_path = os.path.join(CROP_DIR, crop_name) |
| try: |
| crop = crop_with_min_size(img, *box) |
| crop.save(crop_path) |
| crop_paths.append(crop_path) |
| except Exception as e: |
| return None, f"crop {image_id} box{idx}: {e}" |
|
|
| if not crop_paths: |
| return None, None |
|
|
| return { |
| "image_path": img_path, |
| "class_name": class_name, |
| "split": split, |
| "crop_image_paths": crop_paths, |
| }, None |
|
|
|
|
| def convert_record(record): |
| img_path_rel = remove_root_prefix(record["image_path"], BASE_DIR) |
| crop_paths_rel = [remove_root_prefix(p, BASE_DIR) for p in record["crop_image_paths"]] |
| tgt_img_path = crop_paths_rel if len(crop_paths_rel) <= 1 else [crop_paths_rel] |
|
|
| return { |
| "qry_inst": "<|image_1|> Locate the specific region that corresponds to the provided text description.", |
| "qry_text": record["class_name"], |
| "qry_img_path": img_path_rel, |
| "tgt_inst": "Match the target", |
| "tgt_text": ["<|image_1|>\n"], |
| "tgt_img_path": tgt_img_path, |
| } |
|
|
|
|
| def sample_test_data(data, max_samples, seed=RANDOM_SEED): |
| if len(data) <= max_samples: |
| return data |
|
|
| rng = random.Random(seed) |
| path_to_samples = {} |
| for s in data: |
| path_to_samples.setdefault(s["qry_img_path"], []).append(s) |
|
|
| unique_paths = list(path_to_samples.keys()) |
| rng.shuffle(unique_paths) |
|
|
| sampled = [] |
| for path in unique_paths: |
| sampled.append(rng.choice(path_to_samples[path])) |
| if len(sampled) >= max_samples: |
| break |
|
|
| if len(sampled) < max_samples: |
| selected_ids = {id(x) for x in sampled} |
| remaining = [x for x in data if id(x) not in selected_ids] |
| rng.shuffle(remaining) |
| sampled.extend(remaining[:max_samples - len(sampled)]) |
|
|
| rng.shuffle(sampled) |
| return sampled |
|
|
|
|
| def main(): |
| os.makedirs(CROP_DIR, exist_ok=True) |
|
|
| with open(CSV_PATH, newline="") as f: |
| rows = list(csv.DictReader(f)) |
| print(f"Raw rows: {len(rows)}") |
|
|
| groups = defaultdict(list) |
| patient_id_map = {} |
| img_split = {} |
| all_categories = set() |
|
|
| for row in rows: |
| if not row.get("resized_xmin", "").strip(): |
| continue |
| categories = ast.literal_eval(row["finding_categories"]) |
| if categories == ["No Finding"]: |
| continue |
|
|
| bbox = ( |
| max(0, int(float(row["resized_xmin"]))), |
| max(0, int(float(row["resized_ymin"]))), |
| max(0, int(float(row["resized_xmax"]))), |
| max(0, int(float(row["resized_ymax"]))), |
| ) |
| image_id = row["image_id"].replace(".png", "") |
| patient_id_map[image_id] = row["patient_id"] |
| img_split[image_id] = row["split"] |
|
|
| for cat in categories: |
| if cat == "No Finding": |
| continue |
| groups[(image_id, cat)].append(bbox) |
| all_categories.add(cat) |
|
|
| cat_to_id = {cat: idx for idx, cat in enumerate(sorted(all_categories))} |
| print(f"Categories ({len(cat_to_id)}): {cat_to_id}") |
|
|
| tasks = [ |
| (key, boxes, cat_to_id[key[1]], patient_id_map[key[0]], img_split[key[0]]) |
| for key, boxes in groups.items() |
| ] |
| print(f"Total groups: {len(tasks)} Workers: {NUM_WORKERS}") |
|
|
| train_records = [] |
| test_records = [] |
| errors = 0 |
|
|
| with Pool(NUM_WORKERS) as pool: |
| for i, (record, err) in enumerate( |
| pool.imap_unordered(process_group, tasks, chunksize=16), start=1 |
| ): |
| if err: |
| print(f" ERROR: {err}") |
| errors += 1 |
| elif record: |
| entry = convert_record(record) |
| if record["split"] == "training": |
| train_records.append(entry) |
| else: |
| test_records.append(entry) |
|
|
| if i % 500 == 0: |
| print(f" [{i}/{len(tasks)}] errors={errors}") |
|
|
| print(f"\nProcessing complete. errors={errors}") |
| print(f" training samples : {len(train_records)}") |
| print(f" test samples (before sampling): {len(test_records)}") |
|
|
| test_records = sample_test_data(test_records, MAX_TEST_SAMPLES, RANDOM_SEED) |
| print(f" test samples (after sampling): {len(test_records)}") |
|
|
| for path, data in [(OUTPUT_TRAIN_JSON, train_records), (OUTPUT_TEST_JSON, test_records)]: |
| os.makedirs(os.path.dirname(path), exist_ok=True) |
| with open(path, "w", encoding="utf-8") as f: |
| json.dump(data, f, ensure_ascii=False, indent=2) |
| print(f" Saved: {path}") |
|
|
|
|
| if __name__ == "__main__": |
| main() |
|
|
